Pre-visualization of the normalized count data before any differential analysis
Allowing multi-threading with up to 4 threads. [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..."
| GF_104w_F_1_2 | GF_104w_F_2_2 | GF_104w_F_3_2 | GF_104w_M_1_2 | GF_104w_M_2_2 | GF_52w_M_1_2 | GF_52w_M_2_2 | GF_52w_M_3_2 | GF_52w_M_4_2 | GF_8w_M_1_2 | ⋯ | SPF_8w_F_4_2 | SPF_8w_F_5_2 | GF_8w_F_1_2 | GF_8w_F_2_2 | GF_8w_F_3_2 | GF_8w_F_4_2 | GF_8w_F_5_2 | GF_104w_M_3_2 | GF_104w_M_5_2 | GF_104w_M_4_2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610005C13Rik | 0.00000 | 0.00000 | 0.00000 | 1.747854 | 1.244311 | 0.8338695 | 4.892544 | 5.547012 | 7.158344 | 8.384882 | ⋯ | 2.57208 | 0.00000 | 18.04370 | 0.00000 | 2.001891 | 5.212621 | 0.00000 | 1.243886 | 1.039189 | 1.495931 |
| 0610007P14Rik | 857.59757 | 740.81613 | 899.06639 | 875.674692 | 981.138840 | 503.6571924 | 525.459208 | 509.215656 | 730.866890 | 597.722277 | ⋯ | 897.65596 | 947.91171 | 888.38701 | 674.46562 | 605.571925 | 586.941079 | 799.60448 | 490.090915 | 592.337898 | 741.981645 |
| 0610009B22Rik | 1008.62104 | 1155.42062 | 1166.35639 | 1210.388671 | 1539.834260 | 1028.9949924 | 867.937277 | 1006.227887 | 869.022923 | 939.106744 | ⋯ | 1280.89590 | 1431.97437 | 1028.49105 | 1009.00917 | 1129.066334 | 949.739473 | 1080.92333 | 685.380950 | 802.254135 | 780.875844 |
| 0610009L18Rik | 27.86743 | 35.77805 | 17.99933 | 20.100317 | 37.951471 | 31.6870419 | 26.419737 | 22.188046 | 4.295006 | 61.089852 | ⋯ | 101.59716 | 71.27956 | 47.76274 | 19.36265 | 11.010399 | 44.828537 | 24.07684 | 24.877711 | 22.862164 | 38.894199 |
| 0610009O20Rik | 214.84887 | 275.70146 | 262.79017 | 223.725271 | 268.771071 | 296.8575505 | 346.392104 | 391.619012 | 306.377109 | 356.956390 | ⋯ | 225.05701 | 182.98632 | 229.26116 | 157.05260 | 268.253349 | 301.289471 | 266.11243 | 334.605219 | 364.755442 | 393.429783 |
| 0610010B08Rik | 0.00000 | 0.00000 | 0.00000 | 0.000000 | 0.000000 | 0.0000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | ⋯ | 0.00000 | 0.00000 | 0.00000 | 0.00000 | 0.000000 | 0.000000 | 0.00000 | 0.000000 | 0.000000 | 0.000000 |
pickSoftThreshold: will use block size 4005. pickSoftThreshold: calculating connectivity for given powers... ..working on genes 1 through 4005 of 11170 ..working on genes 4006 through 8010 of 11170 ..working on genes 8011 through 11170 of 11170 Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. 1 1 0.0868 0.882 0.888 1080.000 1.09e+03 1690.00 2 2 0.2860 -1.170 0.863 336.000 3.22e+02 799.00 3 3 0.5750 -1.720 0.923 133.000 1.16e+02 460.00 4 4 0.6710 -2.020 0.935 61.500 4.70e+01 296.00 5 5 0.7370 -2.100 0.954 31.700 2.09e+01 205.00 6 6 0.7430 -2.220 0.956 17.700 9.85e+00 148.00 7 7 0.7790 -2.190 0.968 10.600 4.92e+00 111.00 8 8 0.7990 -2.150 0.974 6.640 2.53e+00 85.60 9 9 0.8190 -2.120 0.978 4.350 1.35e+00 67.20 10 10 0.8340 -2.050 0.982 2.950 7.41e-01 53.70 11 12 0.8560 -1.950 0.986 1.470 2.38e-01 35.60 12 14 0.8730 -1.870 0.986 0.802 8.27e-02 24.50 13 16 0.8820 -1.800 0.979 0.468 3.12e-02 17.30 14 18 0.9180 -1.690 0.985 0.288 1.19e-02 12.50 15 20 0.9420 -1.600 0.988 0.185 4.79e-03 9.16
| Power | SFT.R.sq | slope | truncated.R.sq | mean.k. | median.k. | max.k. |
|---|---|---|---|---|---|---|
| 1 | 0.08682157 | 0.8820601 | 0.8877917 | 1081.1068565 | 1.089741e+03 | 1686.156755 |
| 2 | 0.28622457 | -1.1729565 | 0.8631891 | 336.3461812 | 3.222064e+02 | 798.575992 |
| 3 | 0.57483023 | -1.7238558 | 0.9230250 | 133.0766539 | 1.155664e+02 | 460.255658 |
| 4 | 0.67059084 | -2.0210959 | 0.9346949 | 61.4749048 | 4.700680e+01 | 296.282031 |
| 5 | 0.73662969 | -2.1024598 | 0.9538173 | 31.6924296 | 2.089565e+01 | 204.558497 |
| 6 | 0.74338186 | -2.2197752 | 0.9564366 | 17.7373675 | 9.852889e+00 | 148.173791 |
| 7 | 0.77934389 | -2.1914854 | 0.9684850 | 10.5815646 | 4.915240e+00 | 111.129137 |
| 8 | 0.79898550 | -2.1545864 | 0.9744351 | 6.6431563 | 2.525501e+00 | 85.561574 |
| 9 | 0.81862291 | -2.1163663 | 0.9783691 | 4.3482460 | 1.346482e+00 | 67.234901 |
| 10 | 0.83443100 | -2.0512651 | 0.9824172 | 2.9466684 | 7.411700e-01 | 53.700873 |
| 12 | 0.85590807 | -1.9520372 | 0.9863926 | 1.4714913 | 2.384285e-01 | 35.566779 |
| 14 | 0.87303836 | -1.8717587 | 0.9862762 | 0.8021158 | 8.270069e-02 | 24.454629 |
| 16 | 0.88236278 | -1.7975866 | 0.9794021 | 0.4677393 | 3.116421e-02 | 17.284522 |
| 18 | 0.91753298 | -1.6901870 | 0.9847788 | 0.2877587 | 1.192253e-02 | 12.479439 |
| 20 | 0.94216559 | -1.6019139 | 0.9880597 | 0.1849243 | 4.786690e-03 | 9.164832 |
| Power | mean.k. | |
|---|---|---|
| 9 | 9 | 4.3482460 |
| 10 | 10 | 2.9466684 |
| 11 | 12 | 1.4714913 |
| 12 | 14 | 0.8021158 |
| 13 | 16 | 0.4677393 |
| 14 | 18 | 0.2877587 |
| 15 | 20 | 0.1849243 |
Parameters for network construction
Calculating module eigengenes block-wise from all genes
Flagging genes and samples with too many missing values...
..step 1
....pre-clustering genes to determine blocks..
Projective K-means:
..k-means clustering..
..merging smaller clusters...
Block sizes:
gBlocks
1 2
7606 3564
..Working on block 1 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 1 into file norm_genes_TOM-block.1.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..removing 2 genes from module 1 because their KME is too low.
..removing 1 genes from module 6 because their KME is too low.
..Working on block 2 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 2 into file norm_genes_TOM-block.2.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..removing 2 genes from module 2 because their KME is too low.
..removing 3 genes from module 4 because their KME is too low.
..merging modules that are too close..
mergeCloseModules: Merging modules whose distance is less than 0.35
Calculating new MEs...
ME0 ME1 ME2 ME3 ME4 ME5 ME6 ME7 ME8 ME9 ME10 ME11 6174 1565 806 781 612 374 324 179 162 80 73 40
TOM calculation: adjacency.. ..will use 4 parallel threads. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done.
| 0610007P14Rik | 0610009B22Rik | 0610009O20Rik | 0610010K14Rik | Mettl26 | 0610030E20Rik | 0610037L13Rik | Fmc1 | 1110004F10Rik | Card19 | ⋯ | Zswim6 | Zswim7 | Zswim8 | Zufsp | Zxda | Zyg11b | Zyx | Zzef1 | Zzz3 | Hikeshi | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610007P14Rik | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 0610009B22Rik | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| 0610009O20Rik | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 0610010K14Rik | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 1 | ⋯ | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 1 |
| Mettl26 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 1 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 0610030E20Rik | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 0 | ⋯ | 1 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 1 | 0 |
[1] 1
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
17799 GO:0090304 6.732271e-37 1 566
5756 GO:0016070 1.348307e-32 1 511
3020 GO:0006139 3.396777e-29 1 581
12953 GO:0046483 6.883528e-28 1 584
4834 GO:0010467 1.653568e-27 1 556
3420 GO:0006725 1.060674e-26 1 585
numInCat term ontology
17799 4325 nucleic acid metabolic process BP
5756 3872 RNA metabolic process BP
3020 4848 nucleobase-containing compound metabolic process BP
12953 4947 heterocycle metabolic process BP
4834 4726 gene expression BP
3420 5011 cellular aromatic compound metabolic process BP
[1] 2
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
16368 GO:0070647 3.091339e-13 1 80
5997 GO:0016567 1.909439e-12 1 67
14460 GO:0051603 2.417010e-12 1 67
8648 GO:0032446 4.636519e-12 1 69
11979 GO:0044257 2.173275e-11 1 67
7417 GO:0030163 2.493776e-11 1 75
numInCat term
16368 694 protein modification by small protein conjugation or removal
5997 541 protein ubiquitination
14460 590 proteolysis involved in cellular protein catabolic process
8648 582 protein modification by small protein conjugation
11979 622 cellular protein catabolic process
7417 745 protein catabolic process
ontology
16368 BP
5997 BP
14460 BP
8648 BP
11979 BP
7417 BP
[1] 3
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
16937 GO:0071704 2.743919e-23 1 490
11965 GO:0044238 4.928763e-23 1 470
3974 GO:0008152 3.120018e-22 1 502
11964 GO:0044237 5.312527e-22 1 466
4377 GO:0009056 2.322063e-20 1 139
12158 GO:0044710 5.886847e-20 1 232
numInCat term ontology
16937 9446 organic substance metabolic process BP
11965 8887 primary metabolic process BP
3974 9868 metabolic process BP
11964 8866 cellular metabolic process BP
4377 1611 catabolic process BP
12158 3454 single-organism metabolic process BP
[1] 4
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
9705 GO:0034641 4.807047e-33 1 250
11964 GO:0044237 1.535082e-32 1 339
3974 GO:0008152 4.655645e-32 1 370
17005 GO:0071840 1.196809e-30 1 233
3590 GO:0007005 2.174423e-30 1 78
3465 GO:0006807 7.690920e-30 1 252
numInCat term ontology
9705 5508 cellular nitrogen compound metabolic process BP
11964 8866 cellular metabolic process BP
3974 9868 metabolic process BP
17005 5620 cellular component organization or biogenesis BP
3590 621 mitochondrion organization BP
3465 5831 nitrogen compound metabolic process BP
[1] 5
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
11972 GO:0044248 1.349996e-10 1 58
12359 GO:0045184 3.791994e-09 1 68
11984 GO:0044265 4.130686e-09 1 40
4378 GO:0009057 7.501194e-09 1 45
4377 GO:0009056 1.754315e-08 1 61
18903 GO:1901575 2.194517e-08 1 59
numInCat term ontology
11972 1304 cellular catabolic process BP
12359 1809 establishment of protein localization BP
11984 793 cellular macromolecule catabolic process BP
4378 980 macromolecule catabolic process BP
4377 1611 catabolic process BP
18903 1540 organic substance catabolic process BP
[1] 6
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
3557 GO:0006952 7.626613e-19 1 66
3560 GO:0006955 2.189496e-18 1 60
1052 GO:0002376 1.020968e-17 1 87
10116 GO:0035456 1.376979e-16 1 15
4620 GO:0009605 5.104588e-15 1 76
3556 GO:0006950 1.960846e-14 1 103
numInCat term ontology
3557 1323 defense response BP
3560 1110 immune response BP
1052 2158 immune system process BP
10116 46 response to interferon-beta BP
4620 1907 response to external stimulus BP
3556 3099 response to stress BP
[1] 7
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
12158 GO:0044710 1.973405e-07 0.9999999 58
13556 GO:0048518 2.788819e-07 0.9999999 74
13560 GO:0048522 1.398066e-06 0.9999994 67
11965 GO:0044238 1.443017e-06 0.9999993 108
5242 GO:0014067 2.674909e-06 1.0000000 4
16937 GO:0071704 3.986056e-06 0.9999981 111
numInCat term
12158 3454 single-organism metabolic process
13556 4974 positive regulation of biological process
13560 4482 positive regulation of cellular process
11965 8887 primary metabolic process
5242 12 negative regulation of phosphatidylinositol 3-kinase signaling
16937 9446 organic substance metabolic process
ontology
12158 BP
13556 BP
13560 BP
11965 BP
5242 BP
16937 BP
[1] 8
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
3468 GO:0006810 2.240896e-05 0.9999895 57
14240 GO:0051234 3.402958e-05 0.9999837 58
3458 GO:0006790 4.123608e-05 0.9999931 10
numInCat term ontology
3468 4082 transport BP
14240 4231 establishment of localization BP
3458 262 sulfur compound metabolic process BP
[1] 9
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 10
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
15 GO:0000028 0 1 8
936 GO:0002181 0 1 9
3177 GO:0006412 0 1 41
3251 GO:0006518 0 1 41
10964 GO:0042255 0 1 9
10976 GO:0042274 0 1 12
numInCat term ontology
15 19 ribosomal small subunit assembly BP
936 49 cytoplasmic translation BP
3177 597 translation BP
3251 738 peptide metabolic process BP
10964 52 ribosome assembly BP
10976 66 ribosomal small subunit biogenesis BP
[1] 11
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 2918 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names)